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R8218/muscleContours.m
fb9e5f2dfcccBashardoust_SystCoord

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muscleContours.m
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%% muscleContours
% This script allows to select the contours on Tiff images of the four
% cuff rotator muscles: Supraspinatus (SS), Infraspinatus (IS), Subscapularis (SC)
% and Teres Minor (TM).
%
% INPUT:
% subject: ### subject number
% type: 'normal' or 'pathologic'
% Author: EPFL-LBO
% Date: 2016-09-05
%%
function [] = muscleContours(subject,type)
directory = 'Z://data'; % Location of the CT database
location = 'P';
CTn = sprintf('P%03d',subject);
listDirInCurrDir = dir([directory '/' CTn(1) '/' CTn(2) '/' CTn(3)]);
listDirInCurrDir = listDirInCurrDir(3:end);
for i=1:length(listDirInCurrDir)
if ~isempty(regexp(listDirInCurrDir(i).name,['^[PN]\d{0,2}[' CTn(4) '][-]\w*'], 'once'))
listDirInCaseFolder = dir([listDirInCurrDir(i).folder '\' listDirInCurrDir(i).name]);
listDirInCaseFolder = listDirInCaseFolder(3:end);
% In all CT folders in the current Case Folder, find CT #1
for j=1:length(listDirInCaseFolder)
if ~isempty(regexp(listDirInCaseFolder(j).name,'^[C][T][-][PN]\d{1,3}[-]\d*[-][1]', 'once'))
outputPath = [listDirInCaseFolder(j).folder '\' listDirInCaseFolder(j).name];
end
end
end
end
pathologic_list = dir(sprintf('%s/%s/P*', directory, location)); %Create the case list
for i = 1:1:numel(pathologic_list) % Loop over the list of patients and extract the complete name of the specific patient
name = pathologic_list(i).name;
t = strfind(name,CTn);
if t == 1;
patient_name = name;
end
end
finaldirectory = [outputPath '\amira\*tif'];
muscleName = cellstr(['SS';'IS';'SC';'TM']);
close all; % Close all figure windows except those created by imtool.
imtool close all; % Close all figure windows created by imtool.
workspace; % Make sure the workspace panel is showing.
fontSize = 16;
imageWindow = [-100 200];
% Choose file
[inputFile, inputPath] = uigetfile(finaldirectory,'Select the image for muscle atrophy measurement');
whereisp = strfind(inputFile, 'P');
if isempty(whereisp)
whereisp = strfind(inputFile, 'N');
if isempty(whereisp)
return
end
end
subject = inputFile(whereisp:whereisp+3);
% Read gray scale image.
inputImage = imread(sprintf('%s%s',inputPath,inputFile));
if size(inputImage,3) == 3
% Calculate the monochrome luminance by combining the RGB values according to the NTSC standard
inputImage = 0.2989*inputImage(:,:,1)...
+0.5870*inputImage(:,:,2)...
+0.1140*inputImage(:,:,3);
end
for i=1:4;
finished = 'Redo';
while strcmp('Redo',finished)
msg = 0; % 0 = no message
% clc; % Clear command window.
close all; % Close all figure windows except those created by imtool.
imtool close all; % Close all figure windows created by imtool.
imshow(inputImage,imageWindow);
imagetitle = sprintf('Select %s ideal section', char(muscleName(i)));
title(imagetitle, 'FontSize', fontSize);
set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
if msg == 1
message = sprintf('Select the ideal section of your muscle in the image. \nLeft click to place points and draw a polygon. Click again on the first point to close the shape.\nYou can move the points once the line is closed. Double-click or right-click and "Create Mask" to finish.');
msg = 0;
uiwait(msgbox(message));
end
binaryImage1 = roipoly();
if isempty(binaryImage1)
error('Invalid selection or interface closed')
end
binaryImage1 = bwmorph(binaryImage1,'majority');
% Get coordinates of the boundary of the polygonal drawn region.
structBoundaries1 = bwboundaries(binaryImage1);
xy1 = structBoundaries1{1}; % Get n by 2 array of x,y coordinates.
x1 = xy1(:, 2); % Columns.
y1 = xy1(:, 1); % Rows.
hold on
plot(x1, y1, 'color','green');
% check contours
finished = questdlg('Please verify the contours. Press "Save" if they are satisfactory or "Redo" if you would like to redo the selection. ',...
'Contour verification','Save','Redo','Save');
end
%% Report results
% mkdir('./results',subject);
if exist([outputPath '\muscles'],'dir') == 0
mkdir(outputPath,'muscles');
end
outputPath2 = [outputPath '\muscles\' char(muscleName(i)) '\'];
mkdir(outputPath2);
outputFile = sprintf('ssContours%s',subject);
% Check for overwriting
overwrite = exist(sprintf('%s%s.mat',outputPath2,outputFile), 'file');
switch overwrite
case 2
isoverwrite = questdlg('Overwrite existing file ?', 'Warning', 'No', 'Yes', 'No');
switch isoverwrite
case 'Yes'
save(sprintf('%s%s.mat',outputPath2,outputFile), 'inputImage','binaryImage1')
saveas(gcf,sprintf('%s%s.tif',outputPath2,outputFile))
fprintf('%s%s.mat\n%s%s.tif\n',outputPath2,outputFile,outputPath2,outputFile);
end
case 0
save(sprintf('%s%s.mat',outputPath2,outputFile), 'inputImage','binaryImage1')
saveas(gcf,sprintf('%s%s.tif',outputPath2,outputFile))
fprintf('%s%s.mat\n%s%s.tif\n',outputPath2,outputFile,outputPath2,outputFile);
end
end
close all;
end
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